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Last updated on 2026-08-13 11:51:23 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR | |||||
| r-devel-linux-x86_64-debian-gcc | 0.0-12 | 0.49 | 2.46 | 2.95 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0-12 | 1.22 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0-12 | 1.18 | ERROR | |||
| r-devel-windows-x86_64 | 0.0-12 | 196.00 | 190.00 | 386.00 | ERROR | |
| r-patched-linux-x86_64 | 0.0-12 | 153.98 | 81.90 | 235.88 | OK | |
| r-release-linux-x86_64 | 0.0-12 | 148.81 | 82.70 | 231.51 | OK | |
| r-release-macos-arm64 | 0.0-12 | 32.00 | 24.00 | 56.00 | OK | |
| r-release-macos-x86_64 | 0.0-12 | 11.00 | ERROR | |||
| r-release-windows-x86_64 | 0.0-12 | 196.00 | 120.00 | 316.00 | OK | |
| r-oldrel-macos-arm64 | 0.0-12 | 33.00 | 29.00 | 62.00 | OK | |
| r-oldrel-macos-x86_64 | 0.0-12 | 107.00 | 313.00 | 420.00 | OK | |
| r-oldrel-windows-x86_64 | 0.0-12 | 238.00 | 234.00 | 472.00 | OK |
Version: 0.0-12
Check: package dependencies
Result: ERROR
Package required but not available: ‘dbarts’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-x86_64
Version: 0.0-12
Check: examples
Result: ERROR
Running examples in 'stan4bart-Ex.R' failed
The error most likely occurred in:
> ### Name: stan4bart
> ### Title: Semiparametric Models Using Stan and BART
> ### Aliases: stan4bart
>
> ### ** Examples
>
> # simulate data (extension of Friedman MARS paper)
> # x consists of 10 variables, only first 5 matter
> # x_4 is linear
> f <- function(x)
+ 10 * sin(pi * x[,1] * x[,2]) + 20 * (x[,3] - 0.5)^2 +
+ 10 * x[,4] + 5 * x[,5]
>
> set.seed(99)
> sigma <- 1.0
>
> n <- 100
> n.g.1 <- 5L
> n.g.2 <- 8L
>
> # sample observation level covariates and calculate marginal mean
> x <- matrix(runif(n * 10), n, 10)
> mu.bart <- f(x) - 10 * x[,4]
> mu.fixef <- 10 * x[,4]
>
> # varying intercepts and slopes for first grouping factor
> g.1 <- sample(n.g.1, n, replace = TRUE)
> Sigma.b.1 <- matrix(c(1.5^2, .2, .2, 1^2), 2)
> b.1 <- matrix(rnorm(2 * n.g.1), n.g.1) %*% chol(Sigma.b.1)
>
> # varying intercepts for second grouping factor
> g.2 <- sample(n.g.2, n, replace = TRUE)
> Sigma.b.2 <- as.matrix(1.2)
> b.2 <- rnorm(n.g.2, 0, sqrt(Sigma.b.2))
>
> mu.ranef <- b.1[g.1,1] + x[,4] * b.1[g.1,2] + b.2[g.2]
>
> y <- mu.bart + mu.fixef + mu.ranef + rnorm(n, 0, sigma)
>
> df <- data.frame(y, x, g.1, g.2)
>
> fit <- stan4bart(
+ formula = y ~
+ X4 + # linear component ("fixef")
+ (1 + X4 | g.1) + (1 | g.2) + # multilevel ("ranef")
+ bart(. - g.1 - g.2 - X4), # use bart for other variables
+ verbose = -1, # suppress ALL output
+ # low numbers for illustration
+ data = df,
+ chains = 1, iter = 10, bart_args = list(n.trees = 5))
Error in parse(text = deparse(RNGkind)[-1L]) :
<text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Calls: stan4bart ... validObject -> anyStrings -> isTRUE -> validityMethod -> parse
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.0-12
Check: tests
Result: ERROR
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> Sys.unsetenv("R_TESTS")
> if (require(testthat, quietly = TRUE)) {
+ require(stan4bart)
+ test_check("stan4bart")
+ } else {
+ cat("package 'testthat' not available; cannot run unit tests\n")
+ }
Loading required package: stan4bart
Loading required package: dbarts
Saving _problems/test-01-continuous-19.R
Saving _problems/test-02-binary-18.R
Saving _problems/test-02-binary-89.R
Saving _problems/test-03-na_action-29.R
Saving _problems/test-03-na_action-51.R
Saving _problems/test-04-factor_levels-25.R
Saving _problems/test-05-rng-17.R
Saving _problems/test-05-rng-35.R
Saving _problems/test-06-no_ranef-19.R
Saving _problems/test-06-no_ranef-26.R
Saving _problems/test-07-extractedTrees-19.R
[ FAIL 16 | WARN 0 | SKIP 2 | PASS 32 ]
══ Skipped tests (2) ═══════════════════════════════════════════════════════════
• On CRAN (2): 'test-02-binary.R:33:3', 'test-02-binary.R:128:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-01-continuous.R:16:1'): (code run outside of `test_that()`) ────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-01-continuous.R:16:1
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-02-binary.R:15:3'): extract matches fitted in causal setting model ──
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-02-binary.R:15:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-02-binary.R:85:3'): predict matches supplied data ──────────────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-02-binary.R:85:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-03-na_action.R:24:3'): na.action = na.omit works correctly ─────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-03-na_action.R:24:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-03-na_action.R:46:3'): na.action = na.exclude works correctly ──
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-03-na_action.R:46:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-04-factor_levels.R:21:3'): model fits with empty factor levels ──
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-04-factor_levels.R:21:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-05-rng.R:13:3'): stan4bart with global seed and one thread is reproducible ──
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-05-rng.R:13:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-05-rng.R:30:3'): stan4bart with fixed seed is reproducible ─────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-05-rng.R:30:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-06-no_ranef.R:17:3'): fit issues warning if overparameterized ──
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-06-no_ranef.R:17:3
2. │ └─testthat:::quasi_capture(...)
3. │ ├─testthat (local) .capture(...)
4. │ │ └─base::withCallingHandlers(...)
5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
6. └─stan4bart::stan4bart(...)
7. └─stan4bart:::stan4bart_fit(...)
8. ├─base::eval(control_call)
9. │ └─base::eval(control_call)
10. └─dbarts::dbartsControl(...)
11. └─methods::new(...)
12. ├─methods::initialize(value, ...)
13. └─dbarts (local) initialize(value, ...)
14. ├─methods::callNextMethod()
15. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
16. └─methods::validObject(.Object)
17. ├─methods (local) anyStrings(validityMethod(object))
18. │ └─base::isTRUE(x)
19. └─dbarts (local) validityMethod(object)
20. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-06-no_ranef.R:23:1'): (code run outside of `test_that()`) ──────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-06-no_ranef.R:23:1
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-07-extractedTrees.R:14:3'): stan4bart extracts trees correctly ──
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-07-extractedTrees.R:14:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-09-bartArgs.R:18:3'): bart args are set correctly ──────────────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-09-bartArgs.R:18:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-10-treatment.R:13:3'): works with logical treatment ────────────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-10-treatment.R:13:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-11-callback.R:44:3'): callback is passed sample correctly ──────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-11-callback.R:44:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-11-callback.R:104:3'): callback works with multiple threads ────
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-11-callback.R:104:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
── Error ('test-11-callback.R:159:3'): callback works with multiple dimmed results ──
Error in `parse(text = deparse(RNGkind)[-1L])`: <text>:1:22: unexpected ')'
1: binom.kind = NULL)
^
Backtrace:
▆
1. └─stan4bart::stan4bart(...) at test-11-callback.R:159:3
2. └─stan4bart:::stan4bart_fit(...)
3. ├─base::eval(control_call)
4. │ └─base::eval(control_call)
5. └─dbarts::dbartsControl(...)
6. └─methods::new(...)
7. ├─methods::initialize(value, ...)
8. └─dbarts (local) initialize(value, ...)
9. ├─methods::callNextMethod()
10. └─methods (local) .nextMethod(.Object = .Object, ... = ...)
11. └─methods::validObject(.Object)
12. ├─methods (local) anyStrings(validityMethod(object))
13. │ └─base::isTRUE(x)
14. └─dbarts (local) validityMethod(object)
15. └─base::parse(text = deparse(RNGkind)[-1L])
[ FAIL 16 | WARN 0 | SKIP 2 | PASS 32 ]
Flavor: r-devel-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.